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- PDB-5o0m: Deglycosylated Nogo Receptor with native disulfide structure 3 -

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Basic information

Entry
Database: PDB / ID: 5o0m
TitleDeglycosylated Nogo Receptor with native disulfide structure 3
ComponentsReticulon-4 receptor
KeywordsSIGNALING PROTEIN / nervous system / signaling / leucine-rich repeat domain / disulfide structure
Function / homology
Function and homology information


Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / corpus callosum development / negative chemotaxis ...Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / corpus callosum development / negative chemotaxis / positive regulation of Rho protein signal transduction / axonal growth cone / axonogenesis / positive regulation of GTPase activity / dendritic shaft / axon guidance / presynapse / negative regulation of neuron projection development / signaling receptor activity / heparin binding / growth cone / perikaryon / cell surface receptor signaling pathway / neuron projection / membrane raft / external side of plasma membrane / neuronal cell body / glutamatergic synapse / protein-containing complex binding / cell surface / endoplasmic reticulum / plasma membrane
Similarity search - Function
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Reticulon-4 receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPronker, M.F. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWOVidi 723.012.002 Netherlands
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction.
Authors: Pronker, M.F. / Tas, R.P. / Vlieg, H.C. / Janssen, B.J.C.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulon-4 receptor
B: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1287
Polymers72,0222
Non-polymers1,1065
Water7,584421
1
A: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6754
Polymers36,0111
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reticulon-4 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4543
Polymers36,0111
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.610, 112.070, 115.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reticulon-4 receptor / Nogo receptor / NgR / Nogo-66 receptor / Nogo66 receptor-1 / NgR1


Mass: 36011.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rtn4r, Ngr1, Nogor / Plasmid: pUPE107.03 / Cell (production host): HEK293 / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Variant (production host): GntI-/- / References: UniProt: Q99PI8
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.05 M MIB buffer pH 5.0, 12.5% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→56.03 Å / Num. obs: 48250 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.994 / Rsym value: 0.129 / Net I/σ(I): 6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.503 / Rsym value: 1.054 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZN

1ozn


Resolution: 1.9→56.03 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.2224 2428 5.05 %
Rwork0.1793 --
obs0.1815 48088 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→56.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 70 421 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034828
X-RAY DIFFRACTIONf_angle_d0.8696572
X-RAY DIFFRACTIONf_dihedral_angle_d12.2371752
X-RAY DIFFRACTIONf_chiral_restr0.032748
X-RAY DIFFRACTIONf_plane_restr0.003861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93880.33711460.30762659X-RAY DIFFRACTION99
1.9388-1.9810.32561420.27792594X-RAY DIFFRACTION99
1.981-2.0270.28781210.25992706X-RAY DIFFRACTION99
2.027-2.07770.26891450.22482607X-RAY DIFFRACTION99
2.0777-2.13390.27191430.22032693X-RAY DIFFRACTION99
2.1339-2.19670.23681400.20852627X-RAY DIFFRACTION99
2.1967-2.26760.24821490.20712666X-RAY DIFFRACTION100
2.2676-2.34870.23061300.19192694X-RAY DIFFRACTION100
2.3487-2.44270.23351430.19042655X-RAY DIFFRACTION99
2.4427-2.55390.21231530.18172637X-RAY DIFFRACTION99
2.5539-2.68850.22641230.16982695X-RAY DIFFRACTION99
2.6885-2.85690.21441440.17662676X-RAY DIFFRACTION99
2.8569-3.07750.23581500.18882689X-RAY DIFFRACTION99
3.0775-3.38720.25911380.17112722X-RAY DIFFRACTION99
3.3872-3.87720.15981530.14712730X-RAY DIFFRACTION99
3.8772-4.88450.17491370.12672752X-RAY DIFFRACTION99
4.8845-56.05940.2211710.16922858X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.22841.0684-1.20925.4813-0.26433.6350.15770.0764-0.5382-0.4986-0.2897-0.61120.74280.70580.05610.45940.19460.00130.34340.07840.2502-36.914560.737114.511
25.72470.79170.04175.0034-1.40094.27910.0986-0.1733-0.16630.0251-0.1796-0.10870.24950.3070.05260.21020.0369-0.04050.16710.01850.0933-45.616270.24819.1294
32.04712.5474-1.07346.1266-0.42847.28620.1237-0.1262-0.09530.488-0.08670.22950.2361-0.0554-0.00250.20710.066-0.01730.16760.0320.1807-52.598176.301920.7199
47.82931.3887-1.6978.32781.44138.10410.0471-0.28840.04820.27660.10440.15150.0798-0.1133-0.10610.15440.0702-0.0320.17010.06230.0517-55.560380.620417.5136
52.20650.78080.12764.82041.11776.35030.0076-0.12390.1390.3245-0.07880.1608-0.122-0.17870.02780.19940.0520.00150.13460.01810.1195-56.361885.98914.3252
67.74211.8215-0.03496.05321.36395.49640.0647-0.41360.49340.3165-0.18420.2747-0.3618-0.44680.05370.2450.0749-0.05530.1695-0.00660.1364-62.510292.358312.304
73.52723.379-0.20653.4745-0.6291.9086-0.19570.15150.6342-0.3609-0.09810.0236-0.6967-0.04660.22020.3030.0367-0.10760.23970.04260.2719-58.431797.65817.1925
84.06020.44040.12043.8784-1.87175.1443-0.1604-0.20120.4747-0.1746-0.07510.6913-0.328-0.34330.1930.23610.0407-0.09980.2234-0.04990.3288-72.575497.66471.643
93.02323.27640.49966.6809-2.34472.74340.5664-0.19651.25280.8743-0.18490.6082-0.571-0.6136-0.33740.65850.2274-0.04680.85-0.24621.0908-82.882101.922413.1409
101.9424-0.9128-0.59643.1810.64961.56790.0574-0.2328-0.19950.3170.0326-0.16760.26340.0555-0.07250.2032-0.0191-0.0860.19130.05860.1516-65.438411.994616.6122
112.4832-0.73691.2912.5792-0.71671.746-0.0156-0.14050.22210.1094-0.00390.1889-0.0959-0.11380.02250.1158-0.0220.05210.1381-0.01120.1233-86.20237.38579.0634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 26 through 83 )
2X-RAY DIFFRACTION2chain 'B' and (resid 84 through 136 )
3X-RAY DIFFRACTION3chain 'B' and (resid 137 through 156 )
4X-RAY DIFFRACTION4chain 'B' and (resid 157 through 175 )
5X-RAY DIFFRACTION5chain 'B' and (resid 176 through 213 )
6X-RAY DIFFRACTION6chain 'B' and (resid 214 through 242 )
7X-RAY DIFFRACTION7chain 'B' and (resid 243 through 256 )
8X-RAY DIFFRACTION8chain 'B' and (resid 257 through 306 )
9X-RAY DIFFRACTION9chain 'B' and (resid 307 through 338 )
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 175 )
11X-RAY DIFFRACTION11chain 'A' and (resid 176 through 338 )

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